Chapter 3 Exporting tree with data

3.1 Introduction

The treeio package supports parsing various phylogenetic tree file formats including software outputs that contain evolutionary evidences. Some of the formats are just log file (e.g. PAML and r8s outputs), while some of the others are non-standard formats (e.g. BEAST and MrBayes outputs that introduce square bracket, which was reserved to store comment in standard Nexus format, to store inferences). With treeio, we are now able to parse these files to extract phylogenetic tree and map associated data on the tree structure. Exporting tree structure is easy, users can use as.phyo method defined treeio to convert treedata object to phylo object then using write.tree or write.nexus implemented in ape package (Paradis, Claude, and Strimmer 2004) to export the tree structure as Newick text or Nexus file. This is quite useful for converting non-standard formats to standard format and for extracting tree from software outputs, such as log file.

However, exporting tree with associated data is still challenging. These associated data can be parsed from analysis programs or obtained from external sources (e.g. phenotypic data, experimental data and clinical data). The major obstacle here is that there is no standard format that designed for storing tree with data. NeXML (Vos et al. 2012) maybe the most flexible format, however it is currently not widely supported. Most of the analysis programs in this field rely extensively on Newick string and Nexus format. In my opinion, although BEAST Nexus format9 may not be the best solution, it is currently a good approach for storing heterogeneous associated data. The beauty of the format is that all the annotate elements are stored within square bracket, which is reserved for comments. So that the file can be parsed as standard Nexus by ignoring annotate elements and existing programs should be able to read them.

3.2 Exporting Tree Data to BEAST Nexus Format

3.2.1 Exporting/converting software output

The treeio package provides write.beast to export treedata object as BEAST Nexus file (Bouckaert et al. 2014). With treeio, it is easy to convert software output to BEAST format if the output can be parsed by treeio (see Chapter 1). For example, we can convert NHX file to BEAST file and use NHX tags to color the tree using FigTree10 (Figure 3.1A) or convert CODEML output and use dN/dS, dN or dS to color the tree in FigTree (Figure 3.1B).

Here is an example of converting NHX file to BEAST format:

nhxfile <- system.file("extdata/NHX", "phyldog.nhx", package="treeio")
nhx <- read.nhx(nhxfile)
# write.beast(nhx, file = "phyldog.tree")
write.beast(nhx)
#NEXUS
[R-package treeio, Fri Aug 30 11:34:38 2019]

BEGIN TAXA;
    DIMENSIONS NTAX = 16;
    TAXLABELS
        Prayidae_D27SS7@2825365
        Kephyes_ovata@2606431
        Chuniphyes_multidentata@1277217
        Apolemia_sp_@1353964
        Bargmannia_amoena@263997
        Bargmannia_elongata@946788
        Physonect_sp_@2066767
        Stephalia_dilata@2960089
        Frillagalma_vityazi@1155031
        Resomia_ornicephala@3111757
        Lychnagalma_utricularia@2253871
        Nanomia_bijuga@717864
        Cordagalma_sp_@1525873
        Rhizophysa_filiformis@3073669
        Hydra_magnipapillata@52244
        Ectopleura_larynx@3556167
    ;
END;
BEGIN TREES;
    TRANSLATE
        1   Prayidae_D27SS7@2825365,
        2   Kephyes_ovata@2606431,
        3   Chuniphyes_multidentata@1277217,
        4   Apolemia_sp_@1353964,
        5   Bargmannia_amoena@263997,
        6   Bargmannia_elongata@946788,
        7   Physonect_sp_@2066767,
        8   Stephalia_dilata@2960089,
        9   Frillagalma_vityazi@1155031,
        10  Resomia_ornicephala@3111757,
        11  Lychnagalma_utricularia@2253871,
        12  Nanomia_bijuga@717864,
        13  Cordagalma_sp_@1525873,
        14  Rhizophysa_filiformis@3073669,
        15  Hydra_magnipapillata@52244,
        16  Ectopleura_larynx@3556167
    ;
    TREE * UNTITLED = [&R] (((1[&Ev=S,S=58,ND=0]:0.0682841,(2[&Ev=S,S=69,ND=1]:0.0193941,3[&Ev=S,S=70,ND=2]:0.0121378)[&Ev=S,S=60,ND=3]:0.0217782)[&Ev=S,S=36,ND=4]:0.0607598,((4[&Ev=S,S=31,ND=9]:0.11832,(((5[&Ev=S,S=37,ND=10]:0.0144549,6[&Ev=S,S=38,ND=11]:0.0149723)[&Ev=S,S=33,ND=12]:0.0925388,7[&Ev=S,S=61,ND=13]:0.077429)[&Ev=S,S=24,ND=14]:0.0274637,(8[&Ev=S,S=52,ND=15]:0.0761163,((9[&Ev=S,S=53,ND=16]:0.0906068,10[&Ev=S,S=54,ND=17]:1e-06)[&Ev=S,S=45,ND=18]:1e-06,((11[&Ev=S,S=65,ND=19]:0.120851,12[&Ev=S,S=71,ND=20]:0.133939)[&Ev=S,S=56,ND=21]:1e-06,13[&Ev=S,S=64,ND=22]:0.0693814)[&Ev=S,S=46,ND=23]:1e-06)[&Ev=S,S=40,ND=24]:0.0333823)[&Ev=S,S=35,ND=25]:1e-06)[&Ev=D,S=24,ND=26]:0.0431861)[&Ev=S,S=19,ND=27]:1e-06,14[&Ev=S,S=26,ND=28]:0.22283)[&Ev=S,S=17,ND=29]:0.0292362)[&Ev=D,S=17,ND=8]:0.185603,(15[&Ev=S,S=16,ND=5]:0.0621782,16[&Ev=S,S=15,ND=6]:0.332505)[&Ev=S,S=12,ND=7]:0.185603)[&Ev=S,S=9,ND=30];
END;

Another example of converting CodeML output to BEAST format:

mlcfile <- system.file("extdata/PAML_Codeml", "mlc", package="treeio")
ml <- read.codeml_mlc(mlcfile)
# write.beast(ml, file = "codeml.tree")
write.beast(ml)
#NEXUS
[R-package treeio, Fri Aug 30 11:34:38 2019]

BEGIN TAXA;
    DIMENSIONS NTAX = 15;
    TAXLABELS
        A
        B
        C
        D
        E
        F
        G
        H
        I
        J
        K
        L
        M
        N
        O
    ;
END;
BEGIN TREES;
    TRANSLATE
        1   A,
        2   B,
        3   C,
        4   D,
        5   E,
        6   F,
        7   G,
        8   H,
        9   I,
        10  J,
        11  K,
        12  L,
        13  M,
        14  N,
        15  O
    ;
    TREE * UNTITLED = [&U] (11[&t=0.082,N=1514.9,S=633.1,dN_vs_dS=0.0224,dN=0.002,dS=0.0878,N_x_dN=3,S_x_dS=55.6]:0.081785,14[&t=0.062,N=1514.9,S=633.1,dN_vs_dS=0.0095,dN=7e-04,dS=0.0689,N_x_dN=1,S_x_dS=43.6]:0.062341,(4[&t=0.082,N=1514.9,S=633.1,dN_vs_dS=0.0385,dN=0.0033,dS=0.0849,N_x_dN=5,S_x_dS=53.8]:0.082021,(12[&t=0.006,N=1514.9,S=633.1,dN_vs_dS=1e-04,dN=0,dS=0.0062,N_x_dN=0,S_x_dS=3.9]:0.005508,(10[&t=0.014,N=1514.9,S=633.1,dN_vs_dS=0.0457,dN=7e-04,dS=0.0143,N_x_dN=1,S_x_dS=9]:0.013996,(7[&t=0.046,N=1514.9,S=633.1,dN_vs_dS=0.1621,dN=0.006,dS=0.0373,N_x_dN=9.2,S_x_dS=23.6]:0.045746,((3[&t=0.028,N=1514.9,S=633.1,dN_vs_dS=0.0461,dN=0.0013,dS=0.0282,N_x_dN=2,S_x_dS=17.9]:0.02773,(5[&t=0.031,N=1514.9,S=633.1,dN_vs_dS=0.0641,dN=0.002,dS=0.0305,N_x_dN=3,S_x_dS=19.3]:0.031104,15[&t=0.048,N=1514.9,S=633.1,dN_vs_dS=0.0538,dN=0.0026,dS=0.0485,N_x_dN=4,S_x_dS=30.7]:0.048389)23[&t=0.008,N=1514.9,S=633.1,dN_vs_dS=1e-04,dN=0,dS=0.0094,N_x_dN=0,S_x_dS=6]:0.008328)22[&t=0.016,N=1514.9,S=633.1,dN_vs_dS=0.0395,dN=7e-04,dS=0.0165,N_x_dN=1,S_x_dS=10.4]:0.015959,(8[&t=0.021,N=1514.9,S=633.1,dN_vs_dS=0.1028,dN=0.002,dS=0.0191,N_x_dN=3,S_x_dS=12.1]:0.021007,(9[&t=0.015,N=1514.9,S=633.1,dN_vs_dS=1e-04,dN=0,dS=0.0167,N_x_dN=0,S_x_dS=10.6]:0.014739,(2[&t=0.032,N=1514.9,S=633.1,dN_vs_dS=1e-04,dN=0,dS=0.0358,N_x_dN=0,S_x_dS=22.7]:0.031643,(1[&t=0.01,N=1514.9,S=633.1,dN_vs_dS=0.0646,dN=7e-04,dS=0.0101,N_x_dN=1,S_x_dS=6.4]:0.01034,(6[&t=0.007,N=1514.9,S=633.1,dN_vs_dS=0.298,dN=0.0013,dS=0.0044,N_x_dN=2,S_x_dS=2.8]:0.006649,13[&t=0.009,N=1514.9,S=633.1,dN_vs_dS=0.0738,dN=7e-04,dS=0.0088,N_x_dN=1,S_x_dS=5.6]:0.009195)28[&t=0.028,N=1514.9,S=633.1,dN_vs_dS=0.0453,dN=0.0013,dS=0.0289,N_x_dN=2,S_x_dS=18.3]:0.028303)27[&t=0.008,N=1514.9,S=633.1,dN_vs_dS=0.0863,dN=7e-04,dS=0.0076,N_x_dN=1,S_x_dS=4.8]:0.008072)26[&t=0.003,N=1514.9,S=633.1,dN_vs_dS=1.5591,dN=0.0013,dS=8e-04,N_x_dN=2,S_x_dS=0.5]:0.0035)25[&t=0.02,N=1514.9,S=633.1,dN_vs_dS=1e-04,dN=0,dS=0.023,N_x_dN=0,S_x_dS=14.6]:0.020359)24[&t=0.001,N=1514.9,S=633.1,dN_vs_dS=1e-04,dN=0,dS=6e-04,N_x_dN=0,S_x_dS=0.4]:0.000555)21[&t=0.024,N=1514.9,S=633.1,dN_vs_dS=0.0549,dN=0.0013,dS=0.0237,N_x_dN=2,S_x_dS=15]:0.023675)20[&t=0.046,N=1514.9,S=633.1,dN_vs_dS=0.0419,dN=0.002,dS=0.047,N_x_dN=3,S_x_dS=29.8]:0.045745)19[&t=0.015,N=1514.9,S=633.1,dN_vs_dS=1e-04,dN=0,dS=0.0166,N_x_dN=0,S_x_dS=10.5]:0.014684)18[&t=0.059,N=1514.9,S=633.1,dN_vs_dS=0.0964,dN=0.0053,dS=0.0545,N_x_dN=8,S_x_dS=34.5]:0.059308)17[&t=0.232,N=1514.9,S=633.1,dN_vs_dS=0.0129,dN=0.0033,dS=0.2541,N_x_dN=5,S_x_dS=160.9]:0.231628)16;
END;
Visualizing BEAST file in FigTree. Directly visualizing NHX file (A) and CodeML output (B) in FigTree is not supported. treeio can convert these files to BEAST compatible NEXUS format which can be directly opened in FigTree and visualized annotated data.

Figure 3.1: Visualizing BEAST file in FigTree. Directly visualizing NHX file (A) and CodeML output (B) in FigTree is not supported. treeio can convert these files to BEAST compatible NEXUS format which can be directly opened in FigTree and visualized annotated data.

3.2.2 Combining tree with external data

Using the utilities provided by tidytree and treeio, it is easy to link external data onto the corresponding phylogeny. The write.beast function enable users to export the tree with external data to a single tree file.

phylo <- as.phylo(nhx)
## print the newick text
write.tree(phylo)
[1] "(((Prayidae_D27SS7@2825365:0.0682841,(Kephyes_ovata@2606431:0.0193941,Chuniphyes_multidentata@1277217:0.0121378):0.0217782):0.0607598,((Apolemia_sp_@1353964:0.11832,(((Bargmannia_amoena@263997:0.0144549,Bargmannia_elongata@946788:0.0149723):0.0925388,Physonect_sp_@2066767:0.077429):0.0274637,(Stephalia_dilata@2960089:0.0761163,((Frillagalma_vityazi@1155031:0.0906068,Resomia_ornicephala@3111757:1e-06):1e-06,((Lychnagalma_utricularia@2253871:0.120851,Nanomia_bijuga@717864:0.133939):1e-06,Cordagalma_sp_@1525873:0.0693814):1e-06):0.0333823):1e-06):0.0431861):1e-06,Rhizophysa_filiformis@3073669:0.22283):0.0292362):0.185603,(Hydra_magnipapillata@52244:0.0621782,Ectopleura_larynx@3556167:0.332505):0.185603);"
N <- Nnode2(phylo)
fake_data <- tibble(node = 1:N, fake_trait = rnorm(N), another_trait = runif(N))
fake_tree <- full_join(phylo, fake_data, by = "node")
write.beast(fake_tree)
#NEXUS
[R-package treeio, Fri Aug 30 11:34:41 2019]

BEGIN TAXA;
    DIMENSIONS NTAX = 16;
    TAXLABELS
        Prayidae_D27SS7@2825365
        Kephyes_ovata@2606431
        Chuniphyes_multidentata@1277217
        Apolemia_sp_@1353964
        Bargmannia_amoena@263997
        Bargmannia_elongata@946788
        Physonect_sp_@2066767
        Stephalia_dilata@2960089
        Frillagalma_vityazi@1155031
        Resomia_ornicephala@3111757
        Lychnagalma_utricularia@2253871
        Nanomia_bijuga@717864
        Cordagalma_sp_@1525873
        Rhizophysa_filiformis@3073669
        Hydra_magnipapillata@52244
        Ectopleura_larynx@3556167
    ;
END;
BEGIN TREES;
    TRANSLATE
        1   Prayidae_D27SS7@2825365,
        2   Kephyes_ovata@2606431,
        3   Chuniphyes_multidentata@1277217,
        4   Apolemia_sp_@1353964,
        5   Bargmannia_amoena@263997,
        6   Bargmannia_elongata@946788,
        7   Physonect_sp_@2066767,
        8   Stephalia_dilata@2960089,
        9   Frillagalma_vityazi@1155031,
        10  Resomia_ornicephala@3111757,
        11  Lychnagalma_utricularia@2253871,
        12  Nanomia_bijuga@717864,
        13  Cordagalma_sp_@1525873,
        14  Rhizophysa_filiformis@3073669,
        15  Hydra_magnipapillata@52244,
        16  Ectopleura_larynx@3556167
    ;
    TREE * UNTITLED = [&R] (((1[&fake_trait=-0.118140158479532,another_trait=0.358319966588169]:0.0682841,(2[&fake_trait=-1.02308336346315,another_trait=0.178163790609688]:0.0193941,3[&fake_trait=0.103599672229184,another_trait=0.93473564600572]:0.0121378)[&fake_trait=-0.59581303574252,another_trait=0.922105083474889]:0.0217782)[&fake_trait=-0.300012313113108,another_trait=0.119739749003202]:0.0607598,(14[&fake_trait=0.589053316158453,another_trait=0.565819646697491]:0.22283,(4[&fake_trait=-0.765460180119788,another_trait=0.888429019600153]:0.11832,((7[&fake_trait=-0.306908277375037,another_trait=0.650574740953743]:0.077429,(5[&fake_trait=-0.357587376956114,another_trait=0.547185462666675]:0.0144549,6[&fake_trait=0.582576884787801,another_trait=0.00538489152677357]:0.0149723)[&fake_trait=1.68690137848482,another_trait=0.634304485516623]:0.0925388)[&fake_trait=1.00444824814337,another_trait=0.420116872293875]:0.0274637,(8[&fake_trait=1.10912385375853,another_trait=0.583255837904289]:0.0761163,((9[&fake_trait=-0.707380205642954,another_trait=0.808900895994157]:0.0906068,10[&fake_trait=0.838100693609065,another_trait=0.0142157829832286]:1e-06)[&fake_trait=-0.509864481867074,another_trait=0.939013464609161]:1e-06,(13[&fake_trait=1.56583127248603,another_trait=0.0454649559687823]:0.0693814,(11[&fake_trait=1.45882763141046,another_trait=0.516774294432253]:0.120851,12[&fake_trait=2.43471798636817,another_trait=0.00467536062933505]:0.133939)[&fake_trait=-1.07656365665571,another_trait=0.518969761673361]:1e-06)[&fake_trait=-1.48426105861817,another_trait=0.044428545050323]:1e-06)[&fake_trait=0.409198668366587,another_trait=0.538205695804209]:0.0333823)[&fake_trait=-0.692527146833782,another_trait=0.58515489147976]:1e-06)[&fake_trait=-1.41216094329287,another_trait=0.935482121771201]:0.0431861)[&fake_trait=1.65980403458888,another_trait=0.125082567567006]:1e-06)[&fake_trait=0.476325081878056,another_trait=0.262554442277178]:0.0292362)[&fake_trait=1.15832764983724,another_trait=0.646949481917545]:0.185603,(15[&fake_trait=0.704447323258862,another_trait=0.663062628591433]:0.0621782,16[&fake_trait=-0.659190065346089,another_trait=0.505218442762271]:0.332505)[&fake_trait=-1.04282102019802,another_trait=0.641324875177816]:0.185603)[&fake_trait=-0.479609047683268,another_trait=0.519890103489161];
END;

After merging, the fake_trait and another_trait stored in fake_data will be linked to the tree, phylo, and store in the treedata object, the fake_tree. The write.beast() function export the tree with associated data to a single BEAST format file. The associated data can be used to visualized the tree using ggtree (Figure 5.7) or FigTree (Figure 3.1).

3.2.3 Merging tree data from different sources

Not only Newick tree text can be combined with associated data, but also tree data obtained from software output can be combined with external data, as well as different tree objects can be merged together (for details, see Chapter 2).

## combine tree object with data
tree_with_data <- full_join(nhx, fake_data, by = "node")
tree_with_data
## 'treedata' S4 object that stored information of
##  '/home/ygc/R/library/treeio/extdata/NHX/phyldog.nhx'.
## 
## ...@ phylo: 
## Phylogenetic tree with 16 tips and 15 internal nodes.
## 
## Tip labels:
##  Prayidae_D27SS7@2825365, Kephyes_ovata@2606431, Chuniphyes_multidentata@1277217, Apolemia_sp_@1353964, Bargmannia_amoena@263997, Bargmannia_elongata@946788, ...
## 
## Rooted; includes branch lengths.
## 
## with the following features available:
##  'Ev',   'S',    'ND',   'fake_trait',   'another_trait'.
## merge two tree object
tree2 <- merge_tree(nhx, fake_tree)
tree2
## 'treedata' S4 object that stored information of
##  '/home/ygc/R/library/treeio/extdata/NHX/phyldog.nhx'.
## 
## ...@ phylo: 
## Phylogenetic tree with 16 tips and 15 internal nodes.
## 
## Tip labels:
##  Prayidae_D27SS7@2825365, Kephyes_ovata@2606431, Chuniphyes_multidentata@1277217, Apolemia_sp_@1353964, Bargmannia_amoena@263997, Bargmannia_elongata@946788, ...
## 
## Rooted; includes branch lengths.
## 
## with the following features available:
##  'Ev',   'S',    'ND',   'fake_trait',   'another_trait'.
identical(tree_with_data, tree2)
## [1] TRUE

After merging data from different sources, the tree with the associated data can be exported into a single file.

write.beast(tree2)
#NEXUS
[R-package treeio, Fri Aug 30 11:34:41 2019]

BEGIN TAXA;
    DIMENSIONS NTAX = 16;
    TAXLABELS
        Prayidae_D27SS7@2825365
        Kephyes_ovata@2606431
        Chuniphyes_multidentata@1277217
        Apolemia_sp_@1353964
        Bargmannia_amoena@263997
        Bargmannia_elongata@946788
        Physonect_sp_@2066767
        Stephalia_dilata@2960089
        Frillagalma_vityazi@1155031
        Resomia_ornicephala@3111757
        Lychnagalma_utricularia@2253871
        Nanomia_bijuga@717864
        Cordagalma_sp_@1525873
        Rhizophysa_filiformis@3073669
        Hydra_magnipapillata@52244
        Ectopleura_larynx@3556167
    ;
END;
BEGIN TREES;
    TRANSLATE
        1   Prayidae_D27SS7@2825365,
        2   Kephyes_ovata@2606431,
        3   Chuniphyes_multidentata@1277217,
        4   Apolemia_sp_@1353964,
        5   Bargmannia_amoena@263997,
        6   Bargmannia_elongata@946788,
        7   Physonect_sp_@2066767,
        8   Stephalia_dilata@2960089,
        9   Frillagalma_vityazi@1155031,
        10  Resomia_ornicephala@3111757,
        11  Lychnagalma_utricularia@2253871,
        12  Nanomia_bijuga@717864,
        13  Cordagalma_sp_@1525873,
        14  Rhizophysa_filiformis@3073669,
        15  Hydra_magnipapillata@52244,
        16  Ectopleura_larynx@3556167
    ;
    TREE * UNTITLED = [&R] (((1[&Ev=S,S=58,ND=0,fake_trait=-0.118140158479532,another_trait=0.358319966588169]:0.0682841,(2[&Ev=S,S=69,ND=1,fake_trait=-1.02308336346315,another_trait=0.178163790609688]:0.0193941,3[&Ev=S,S=70,ND=2,fake_trait=0.103599672229184,another_trait=0.93473564600572]:0.0121378)[&Ev=S,S=60,ND=3,fake_trait=-0.59581303574252,another_trait=0.922105083474889]:0.0217782)[&Ev=S,S=36,ND=4,fake_trait=-0.300012313113108,another_trait=0.119739749003202]:0.0607598,((4[&Ev=S,S=31,ND=9,fake_trait=-0.765460180119788,another_trait=0.888429019600153]:0.11832,(((5[&Ev=S,S=37,ND=10,fake_trait=-0.357587376956114,another_trait=0.547185462666675]:0.0144549,6[&Ev=S,S=38,ND=11,fake_trait=0.582576884787801,another_trait=0.00538489152677357]:0.0149723)[&Ev=S,S=33,ND=12,fake_trait=1.68690137848482,another_trait=0.634304485516623]:0.0925388,7[&Ev=S,S=61,ND=13,fake_trait=-0.306908277375037,another_trait=0.650574740953743]:0.077429)[&Ev=S,S=24,ND=14,fake_trait=1.00444824814337,another_trait=0.420116872293875]:0.0274637,(8[&Ev=S,S=52,ND=15,fake_trait=1.10912385375853,another_trait=0.583255837904289]:0.0761163,((9[&Ev=S,S=53,ND=16,fake_trait=-0.707380205642954,another_trait=0.808900895994157]:0.0906068,10[&Ev=S,S=54,ND=17,fake_trait=0.838100693609065,another_trait=0.0142157829832286]:1e-06)[&Ev=S,S=45,ND=18,fake_trait=-0.509864481867074,another_trait=0.939013464609161]:1e-06,((11[&Ev=S,S=65,ND=19,fake_trait=1.45882763141046,another_trait=0.516774294432253]:0.120851,12[&Ev=S,S=71,ND=20,fake_trait=2.43471798636817,another_trait=0.00467536062933505]:0.133939)[&Ev=S,S=56,ND=21,fake_trait=-1.07656365665571,another_trait=0.518969761673361]:1e-06,13[&Ev=S,S=64,ND=22,fake_trait=1.56583127248603,another_trait=0.0454649559687823]:0.0693814)[&Ev=S,S=46,ND=23,fake_trait=-1.48426105861817,another_trait=0.044428545050323]:1e-06)[&Ev=S,S=40,ND=24,fake_trait=0.409198668366587,another_trait=0.538205695804209]:0.0333823)[&Ev=S,S=35,ND=25,fake_trait=-0.692527146833782,another_trait=0.58515489147976]:1e-06)[&Ev=D,S=24,ND=26,fake_trait=-1.41216094329287,another_trait=0.935482121771201]:0.0431861)[&Ev=S,S=19,ND=27,fake_trait=1.65980403458888,another_trait=0.125082567567006]:1e-06,14[&Ev=S,S=26,ND=28,fake_trait=0.589053316158453,another_trait=0.565819646697491]:0.22283)[&Ev=S,S=17,ND=29,fake_trait=0.476325081878056,another_trait=0.262554442277178]:0.0292362)[&Ev=D,S=17,ND=8,fake_trait=1.15832764983724,another_trait=0.646949481917545]:0.185603,(15[&Ev=S,S=16,ND=5,fake_trait=0.704447323258862,another_trait=0.663062628591433]:0.0621782,16[&Ev=S,S=15,ND=6,fake_trait=-0.659190065346089,another_trait=0.505218442762271]:0.332505)[&Ev=S,S=12,ND=7,fake_trait=-1.04282102019802,another_trait=0.641324875177816]:0.185603)[&Ev=S,S=9,ND=30,fake_trait=-0.479609047683268,another_trait=0.519890103489161];
END;

The output BEAST Nexus file can be imported into R using the read.beast function and all the associated data can be used to annotate the tree using ggtree (Yu et al. 2017).

outfile <- tempfile(fileext = ".tree")
write.beast(tree2, file = outfile)
read.beast(outfile)
## 'treedata' S4 object that stored information of
##  '/tmp/RtmpUfeAdI/file2ed07b7afbab.tree'.
## 
## ...@ phylo: 
## Phylogenetic tree with 16 tips and 15 internal nodes.
## 
## Tip labels:
##  Prayidae_D27SS7@2825365, Kephyes_ovata@2606431, Chuniphyes_multidentata@1277217, Apolemia_sp_@1353964, Bargmannia_amoena@263997, Bargmannia_elongata@946788, ...
## 
## Rooted; includes branch lengths.
## 
## with the following features available:
##  'another_trait',    'Ev',   'fake_trait',   'ND',   'S'.

3.3 Exporting Tree Data to jtree Format

The treeio package provides write.beast to export treedata to BEAST Nexus file. This is quite useful to convert file format, combine tree with data and merging tree data from different sources as we demonstrated in session 3.2. The treeio package also supplies read.beast function to parse output file of write.beast. Although with treeio, the R community has the ability to manipulate BEAST Nexus format and process tree data, there is still lacking library/package for parsing BEAST file in other programming language.

JSON (JavaScript Object Notation) is a lightweight data-interchange format and widely supported in almost all modern programming languages. To make it easy to import tree with data in other programming languages, treeio supports exporting tree with data in jtree format, which is JSON-based and can be easy to parse using any languages that supports JSON.

write.jtree(tree2)
{
    "tree": "(((Prayidae_D27SS7@2825365:0.0682841{1},(Kephyes_ovata@2606431:0.0193941{2},Chuniphyes_multidentata@1277217:0.0121378{3}):0.0217782{20}):0.0607598{19},((Apolemia_sp_@1353964:0.11832{4},(((Bargmannia_amoena@263997:0.0144549{5},Bargmannia_elongata@946788:0.0149723{6}):0.0925388{25},Physonect_sp_@2066767:0.077429{7}):0.0274637{24},(Stephalia_dilata@2960089:0.0761163{8},((Frillagalma_vityazi@1155031:0.0906068{9},Resomia_ornicephala@3111757:1{10}e-06):1{28}e-06,((Lychnagalma_utricularia@2253871:0.120851{11},Nanomia_bijuga@717864:0.133939{12}):1{30}e-06,Cordagalma_sp_@1525873:0.0693814{13}):1{29}e-06):0.0333823{27}):1{26}e-06):0.0431861{23}):1{22}e-06,Rhizophysa_filiformis@3073669:0.22283{14}):0.0292362{21}):0.185603{18},(Hydra_magnipapillata@52244:0.0621782{15},Ectopleura_larynx@3556167:0.332505{16}):0.185603{31}){17};",
    "data":[
  {
    "edge_num": 1,
    "Ev": "S",
    "S": "58",
    "ND": 0,
    "fake_trait": -0.1181,
    "another_trait": 0.3583
  },
  {
    "edge_num": 2,
    "Ev": "S",
    "S": "69",
    "ND": 1,
    "fake_trait": -1.0231,
    "another_trait": 0.1782
  },
  {
    "edge_num": 3,
    "Ev": "S",
    "S": "70",
    "ND": 2,
    "fake_trait": 0.1036,
    "another_trait": 0.9347
  },
  {
    "edge_num": 4,
    "Ev": "S",
    "S": "31",
    "ND": 9,
    "fake_trait": -0.7655,
    "another_trait": 0.8884
  },
  {
    "edge_num": 5,
    "Ev": "S",
    "S": "37",
    "ND": 10,
    "fake_trait": -0.3576,
    "another_trait": 0.5472
  },
  {
    "edge_num": 6,
    "Ev": "S",
    "S": "38",
    "ND": 11,
    "fake_trait": 0.5826,
    "another_trait": 0.0054
  },
  {
    "edge_num": 7,
    "Ev": "S",
    "S": "61",
    "ND": 13,
    "fake_trait": -0.3069,
    "another_trait": 0.6506
  },
  {
    "edge_num": 8,
    "Ev": "S",
    "S": "52",
    "ND": 15,
    "fake_trait": 1.1091,
    "another_trait": 0.5833
  },
  {
    "edge_num": 9,
    "Ev": "S",
    "S": "53",
    "ND": 16,
    "fake_trait": -0.7074,
    "another_trait": 0.8089
  },
  {
    "edge_num": 10,
    "Ev": "S",
    "S": "54",
    "ND": 17,
    "fake_trait": 0.8381,
    "another_trait": 0.0142
  },
  {
    "edge_num": 11,
    "Ev": "S",
    "S": "65",
    "ND": 19,
    "fake_trait": 1.4588,
    "another_trait": 0.5168
  },
  {
    "edge_num": 12,
    "Ev": "S",
    "S": "71",
    "ND": 20,
    "fake_trait": 2.4347,
    "another_trait": 0.0047
  },
  {
    "edge_num": 13,
    "Ev": "S",
    "S": "64",
    "ND": 22,
    "fake_trait": 1.5658,
    "another_trait": 0.0455
  },
  {
    "edge_num": 14,
    "Ev": "S",
    "S": "26",
    "ND": 28,
    "fake_trait": 0.5891,
    "another_trait": 0.5658
  },
  {
    "edge_num": 15,
    "Ev": "S",
    "S": "16",
    "ND": 5,
    "fake_trait": 0.7044,
    "another_trait": 0.6631
  },
  {
    "edge_num": 16,
    "Ev": "S",
    "S": "15",
    "ND": 6,
    "fake_trait": -0.6592,
    "another_trait": 0.5052
  },
  {
    "edge_num": 17,
    "Ev": "S",
    "S": "9",
    "ND": 30,
    "fake_trait": -0.4796,
    "another_trait": 0.5199
  },
  {
    "edge_num": 18,
    "Ev": "D",
    "S": "17",
    "ND": 8,
    "fake_trait": 1.1583,
    "another_trait": 0.6469
  },
  {
    "edge_num": 19,
    "Ev": "S",
    "S": "36",
    "ND": 4,
    "fake_trait": -0.3,
    "another_trait": 0.1197
  },
  {
    "edge_num": 20,
    "Ev": "S",
    "S": "60",
    "ND": 3,
    "fake_trait": -0.5958,
    "another_trait": 0.9221
  },
  {
    "edge_num": 21,
    "Ev": "S",
    "S": "17",
    "ND": 29,
    "fake_trait": 0.4763,
    "another_trait": 0.2626
  },
  {
    "edge_num": 22,
    "Ev": "S",
    "S": "19",
    "ND": 27,
    "fake_trait": 1.6598,
    "another_trait": 0.1251
  },
  {
    "edge_num": 23,
    "Ev": "D",
    "S": "24",
    "ND": 26,
    "fake_trait": -1.4122,
    "another_trait": 0.9355
  },
  {
    "edge_num": 24,
    "Ev": "S",
    "S": "24",
    "ND": 14,
    "fake_trait": 1.0044,
    "another_trait": 0.4201
  },
  {
    "edge_num": 25,
    "Ev": "S",
    "S": "33",
    "ND": 12,
    "fake_trait": 1.6869,
    "another_trait": 0.6343
  },
  {
    "edge_num": 26,
    "Ev": "S",
    "S": "35",
    "ND": 25,
    "fake_trait": -0.6925,
    "another_trait": 0.5852
  },
  {
    "edge_num": 27,
    "Ev": "S",
    "S": "40",
    "ND": 24,
    "fake_trait": 0.4092,
    "another_trait": 0.5382
  },
  {
    "edge_num": 28,
    "Ev": "S",
    "S": "45",
    "ND": 18,
    "fake_trait": -0.5099,
    "another_trait": 0.939
  },
  {
    "edge_num": 29,
    "Ev": "S",
    "S": "46",
    "ND": 23,
    "fake_trait": -1.4843,
    "another_trait": 0.0444
  },
  {
    "edge_num": 30,
    "Ev": "S",
    "S": "56",
    "ND": 21,
    "fake_trait": -1.0766,
    "another_trait": 0.519
  },
  {
    "edge_num": 31,
    "Ev": "S",
    "S": "12",
    "ND": 7,
    "fake_trait": -1.0428,
    "another_trait": 0.6413
  }
],
    "metadata": {"info": "R-package treeio", "data": "Fri Aug 30 11:34:41 2019"}
}

The jtree format is based on JSON and can be parsed using JSON parser.

jtree_file <- tempfile(fileext = '.jtree')
write.jtree(tree2, file = jtree_file)
jsonlite::fromJSON(jtree_file)
$tree
[1] "(((Prayidae_D27SS7@2825365:0.0682841{1},(Kephyes_ovata@2606431:0.0193941{2},Chuniphyes_multidentata@1277217:0.0121378{3}):0.0217782{20}):0.0607598{19},((Apolemia_sp_@1353964:0.11832{4},(((Bargmannia_amoena@263997:0.0144549{5},Bargmannia_elongata@946788:0.0149723{6}):0.0925388{25},Physonect_sp_@2066767:0.077429{7}):0.0274637{24},(Stephalia_dilata@2960089:0.0761163{8},((Frillagalma_vityazi@1155031:0.0906068{9},Resomia_ornicephala@3111757:1{10}e-06):1{28}e-06,((Lychnagalma_utricularia@2253871:0.120851{11},Nanomia_bijuga@717864:0.133939{12}):1{30}e-06,Cordagalma_sp_@1525873:0.0693814{13}):1{29}e-06):0.0333823{27}):1{26}e-06):0.0431861{23}):1{22}e-06,Rhizophysa_filiformis@3073669:0.22283{14}):0.0292362{21}):0.185603{18},(Hydra_magnipapillata@52244:0.0621782{15},Ectopleura_larynx@3556167:0.332505{16}):0.185603{31}){17};"

$data
   edge_num Ev  S ND fake_trait another_trait
1         1  S 58  0    -0.1181        0.3583
2         2  S 69  1    -1.0231        0.1782
3         3  S 70  2     0.1036        0.9347
4         4  S 31  9    -0.7655        0.8884
5         5  S 37 10    -0.3576        0.5472
6         6  S 38 11     0.5826        0.0054
7         7  S 61 13    -0.3069        0.6506
8         8  S 52 15     1.1091        0.5833
9         9  S 53 16    -0.7074        0.8089
10       10  S 54 17     0.8381        0.0142
11       11  S 65 19     1.4588        0.5168
12       12  S 71 20     2.4347        0.0047
13       13  S 64 22     1.5658        0.0455
14       14  S 26 28     0.5891        0.5658
15       15  S 16  5     0.7044        0.6631
16       16  S 15  6    -0.6592        0.5052
17       17  S  9 30    -0.4796        0.5199
18       18  D 17  8     1.1583        0.6469
19       19  S 36  4    -0.3000        0.1197
20       20  S 60  3    -0.5958        0.9221
21       21  S 17 29     0.4763        0.2626
22       22  S 19 27     1.6598        0.1251
23       23  D 24 26    -1.4122        0.9355
24       24  S 24 14     1.0044        0.4201
25       25  S 33 12     1.6869        0.6343
26       26  S 35 25    -0.6925        0.5852
27       27  S 40 24     0.4092        0.5382
28       28  S 45 18    -0.5099        0.9390
29       29  S 46 23    -1.4843        0.0444
30       30  S 56 21    -1.0766        0.5190
31       31  S 12  7    -1.0428        0.6413

$metadata
$metadata$info
[1] "R-package treeio"

$metadata$data
[1] "Fri Aug 30 11:34:41 2019"

The jtree file can be directly imported as a treedata object using read.jtree provided also in treeio package (see also session 1.3).

read.jtree(jtree_file)
## 'treedata' S4 object that stored information of
##  '/tmp/RtmpUfeAdI/file2ed06b2b0c47.jtree'.
## 
## ...@ phylo: 
## Phylogenetic tree with 16 tips and 15 internal nodes.
## 
## Tip labels:
##  Prayidae_D27SS7@2825365, Kephyes_ovata@2606431, Chuniphyes_multidentata@1277217, Apolemia_sp_@1353964, Bargmannia_amoena@263997, Bargmannia_elongata@946788, ...
## 
## Rooted; includes branch lengths.
## 
## with the following features available:
##  'Ev',   'S',    'ND',   'fake_trait',   'another_trait'.

3.4 Summary

Phylogenetic tree associated data is often stored in a separate file and need expertise to map the data to the tree structure. Lacking standardization to store and represent phylogeny and associated data makes it difficult for researchers to access and integrate the phylogenetic data into their studies. The treeio package provides functions to import phylogeny with associated data from a number of sources, including analysis finding from commonly used software and external data such as experimental, clinical or meta data. These tree + data can be exported into a single file as a BEAST or jtree formats, and the output file can be parsed back to R by treeio and the data is easy to access. The input and output utilities supplied by treeio package lay the foundation for phylogenetic data integration for downstream comparative study and visualization.

References

Bouckaert, Remco, Joseph Heled, Denise Kühnert, Tim Vaughan, Chieh-Hsi Wu, Dong Xie, Marc A. Suchard, Andrew Rambaut, and Alexei J. Drummond. 2014. “BEAST 2: A Software Platform for Bayesian Evolutionary Analysis.” PLoS Comput Biol 10 (4): e1003537. https://doi.org/10.1371/journal.pcbi.1003537.

Paradis, Emmanuel, Julien Claude, and Korbinian Strimmer. 2004. “APE: Analyses of Phylogenetics and Evolution in R Language.” Bioinformatics 20 (2): 289–90. https://doi.org/10.1093/bioinformatics/btg412.

Vos, Rutger A., James P. Balhoff, Jason A. Caravas, Mark T. Holder, Hilmar Lapp, Wayne P. Maddison, Peter E. Midford, et al. 2012. “NeXML: Rich, Extensible, and Verifiable Representation of Comparative Data and Metadata.” Systematic Biology 61 (4): 675–89. https://doi.org/10.1093/sysbio/sys025.

Yu, Guangchuang, David K. Smith, Huachen Zhu, Yi Guan, and Tommy Tsan-Yuk Lam. 2017. “Ggtree: An R Package for Visualization and Annotation of Phylogenetic Trees with Their Covariates and Other Associated Data.” Methods in Ecology and Evolution 8 (1): 28–36. https://doi.org/10.1111/2041-210X.12628.